Lipid oxidation takes place in the gastric tract after the ingestion of a Western diet rich in ω-6 polyunsaturated fatty acids (PUFA) and red meat (heme iron). The incorporation of oxidation products such as 4-hydroxy-2-nonenal (4-HNE) into low-density lipoproteins is further correlated to endothelial dysfunction. Gastric postprandial stress could thus be reduced by antioxidant phytomicronutrients. The aim of this study was to investigate dietary lipid oxidation and its inhibition by apple polyphenols under different matrix forms (fresh fruit, puree, extract) under in vitro gastric digestion conditions. A deep insight was given into the two factors pH and pepsin governing the metmyoglobin-initiated lipid oxidation of sunflower oil-in-water emulsions simulating the physical state of dietary lipids. Our results first showed that pepsin accelerated lipid oxidation at pH 5 through the formation of a micro-metmyoglobin form likely displaying a higher accessibility to lipids. Spectroscopic studies further highlighted the formation of a reversible unfolded metmyoglobin form at pH 3 which was shown to be more pro-oxidant in the absence of pepsin. At nutritional levels, the three apple matrices inhibited less efficiently the accumulation of lipid-derived conjugated dienes and 4-HNE at pH 5 when pepsin was present whereas at pH 3 the opposite was true. High initial bioaccessibilities of monomeric phenolic compounds were evidenced for both puree (57–74%) and the phenolic extract (79–96%) compared to fresh apple (1–14%) supporting their greater antioxidant capacity. By contrast, the bioaccessibility of dimer B2 was low for all matrices suggesting non-covalent binding to apple pectins.